ArticleGenome biology2015
Exploring the rice dispensable genome using a metagenome-like assembly strategy.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Pan-genome of wild and cultivated rice uncovers genetic diversity, lost and selected sequences during rice domestication.Rice (New York, N.Y.) · 2026Article
- On the use and misuse of pangenome and related terms.Nature communications · 2026Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Unveiling the Genomic Symphony: Identification Cultivar-Specific Genes and Enhanced Insights on Sweet Sorghum Genomes Through Comprehensive superTranscriptomic Analysis.Journal of molecular evolution · 2024Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
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- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.Animals : an open access journal from MDPI · 2024Article
- Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus).BMC genomic data · 2024Article
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.Genome biology · 2023Article
- PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes.Microbiology spectrum · 2023Article
- Exploring domestication pattern in lotus: insights from dispensable genome assembly.Frontiers in plant science · 2023Article
- Deep polygenic neural network for predicting and identifying yield-associated genes in Indonesian rice accessions.Scientific reports · 2022Article
- Article
- Pangenomics and Crop Genome Adaptation in a Changing Climate.Plants (Basel, Switzerland) · 2022Review
- Pangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs.The plant genome · 2022Review
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe dispensable genome of a species, consisting of the dispensable sequences present only in a subset of individuals, is believed to play important roles in phenotypic variation and genome evolution. However, construction of the dispensable genome is costly and labor-intensive at present, and so the influence of the dispensable genome in genetic and functional genomic studies has not been fully explored.
resultsWe construct the dispensable genome of rice through a metagenome-like de novo assembly strategy based on low-coverage (1-3×) sequencing data of 1483 cultivated rice (Oryza sativa L.) accessions. Thousands of protein-coding genes are successfully assembled, including most of the known agronomically important genes absent from the Nipponbare rice reference genome. We develop an integration approach based on alignment and linkage disequilibrium, which is able to assign genomic positions relative to the reference genome for more than 78.2 % of the dispensable sequences. We carry out association mapping studies for rice grain width and 840 metabolic traits using 0.46 million polymorphisms between the dispensable sequences of different rice accessions. About 23.5 % of metabolic traits have more significant association signals with polymorphisms from dispensable sequences than with SNPs from the reference genome, and 41.6 % of trait-associated SNPs have concordant genomic locations with associated dispensable sequences.
conclusionsOur results suggest the feasibility of building a species' dispensable genome using low-coverage population sequencing data. The constructed sequences will be helpful for understanding the rice dispensable genome and are complementary to the reference genome for identifying candidate genes associated with phenotypic variation.
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